[gmx-users] number of water molecules affects the PMF

[XAvier Periole]

On Jun 2, 2010, at 9:49 AM, Ozge Engin wrote:

> Hi Chris,
>
> The two setups were different from each other in terms of only the  
> number of water molecules. Even the starting
> conformations for the two peptides were the same. I especially took  
> care about that to leave only the number of molecules as a variable.
>
> I calculated the error by dividing the whole data to 4, and  
> calculated the standard deviation between the 4 sets, and divided  
> the result by sqrt (3).
>
> For the Xavier's suggestion: I think I should wait a little, at  
> least until having the same length of trajectory for the two sets.
Here we go! You are probably not converged! How long did you simulate?
>
> Thanks
>
> -- 
> Ozge Engin
> ★☆
> -- 
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